Docker ubuntu-18.04 fails on missing CMakeLists.txt

Question

Docker ubuntu-18.04 fails on missing CMakeLists.txt

alfred-stokespace opened this issue 3 years ago · 16 comments

alfred-stokespace commented 3 years ago

Specific error I get in container

CMake Error: The source directory "/REFPROP-cmake/build" does not appear to contain CMakeLists.txt.

Setup

Host: Dell Precision i7-10850H CPU
Windows: 10 ( HOST OS)
Building on VMWARE: Ubuntu VM ( GUEST OS)

Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal

Build directory in Guest OS

tree -L 1
.
├── Dockerfile
├── Makefile
├── RP10src
└── run-me-inside-container.sh

1 directory, 3 files

My Makefile is just convenience wrapper.

build:
	docker build -t rpub18 .

run:
	docker run -it -v "$$(pwd)":/shared  -t rpub18 bash

I put your readme command into the run-me-inside-container.sh and COPY that into the container in Dockerfile

cd /REFPROP-cmake/build
cmake -DREFPROP_FORTRAN_PATH=/shared/RP10src
cmake --build .

My Dockerfile ...

FROM ubuntu:18.04

RUN apt-get -y -m update && \
    apt-get install -y git cmake g++ gfortran python3 python3-pip

# This ADD block forces a build (invalidates the cache) if the git repo contents have changed, otherwise leaves it untouched.
ADD https://api.github.com/repos/usnistgov/REFPROP-cmake/git/refs/heads/master RPcmake-version.json
RUN git clone --recursive https://github.com/usnistgov/REFPROP-cmake && \
    cd REFPROP-cmake/ && \
    mkdir build && \
    cd build/

# Soft-link pip3->pip and same for python
RUN ln -s /usr/bin/pip3 /usr/bin/pip && \
    ln -s /usr/bin/python3 /usr/bin/python

# Install numpy from pip
RUN pip install numpy && python -c "import numpy; print(numpy.__version__)"

COPY ./run-me-inside-container.sh ./build.sh

I build the Image make build (that's fine)
I issue make run

   docker run -it -v "$(pwd)":/shared  -t rpub18 bash

   root@2f96fd1a1974:/# ./build.sh 
   CMake Error: The source directory "/REFPROP-cmake/build" does not appear to contain CMakeLists.txt.
   Specify --help for usage, or press the help button on the CMake GUI.
   Error: could not load cache
   root@2f96fd1a1974:/#

I confirm the contents of /shared/RP10src/

   root@3e95db2a941f:/# ls /shared/RP10src/
   COMAGA8.INC  COMTRN.INC    DLLFILES      SAT_SUB.FOR   UTILITY.FOR
   COMANC.INC   CONSTS.INC    FLSH_SUB.FOR  SETUP.FOR
   COMFEQ.INC   CORE_ANC.FOR  MIX_HMX.FOR   TRNSP.FOR
   COMMONS.INC  CORE_FEQ.FOR  PROP_SUB.FOR  TRNS_TCX.FOR
   COMREFP.INC  CORE_PR.FOR   REFPROP.FOR   TRNS_VIS.FOR

I confirm the contents of /REFPROP-cmake/build/

   root@3e95db2a941f:/# ls -ltra  /REFPROP-cmake/build/
   total 8
   drwxr-xr-x 6 root root 4096 Jun 16 13:14 ..
   drwxr-xr-x 2 root root 4096 Jun 16 13:14 .
   root@3e95db2a941f:/#

Commentary

I first tried this in a WSL Ubuntu 20.04 and didn't have all the Makefile business and just copy pasted your commands. Same error as the above VMWare attempt.

Answer 1 · 2022-06-16T14:10:10.000Z

You're using cmake wrong. Your commands should read:

cd /REFPROP-cmake/build
cmake .. -DREFPROP_FORTRAN_PATH=/shared/RP10src
cmake --build .

Note the missing .. in the second command

Answer 2 · 2022-06-16T14:17:15.000Z

thanks @ianhbell I'll try that.
your docs suggest the .. isn't necessary

Answer 3 · 2022-06-16T14:20:06.000Z

What README are you referring to?

Answer 4 · 2022-06-16T14:20:40.000Z

https://github.com/usnistgov/REFPROP-cmake/blob/master/docker/ubuntu-18.04/README.md

Answer 5 · 2022-06-16T14:22:12.000Z

Otherwise I think I'm in business

-- DEFSYM_FLAG: --using-defsym
-- linux
Missing from PASS_CMN_tokens:  ['ABFLASHdll', 'VIRBCD12dll', 'VIRTAUdll']
Missing from REFPROP_lib.h: []

-- Configuring done
-- Generating done
-- Build files have been written to: /REFPROP-cmake/build
Scanning dependencies of target refprop
[  6%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/CORE_ANC.FOR.o
[ 12%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/CORE_FEQ.FOR.o
[ 18%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/CORE_PR.FOR.o
[ 25%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/FLSH_SUB.FOR.o
[ 31%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/MIX_HMX.FOR.o
[ 37%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/PROP_SUB.FOR.o
[ 43%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/REFPROP.FOR.o
/shared/RP10src/REFPROP.FOR:5589:72:

          if (ABS(iErrPrnt).eq.3) pause           !If your compiler complains about this line, just delete it.
                                                                        1
Warning: Deleted feature: PAUSE statement at (1)
[ 50%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/SAT_SUB.FOR.o
[ 56%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/SETUP.FOR.o
[ 62%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/TRNSP.FOR.o
[ 68%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/TRNS_TCX.FOR.o
[ 75%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/TRNS_VIS.FOR.o
[ 81%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/UTILITY.FOR.o
[ 87%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/DLLFILES/PASS_FTN.FOR.o
[ 93%] Linking Fortran shared library librefprop.so
[ 93%] Built target refprop
Scanning dependencies of target REFPROP_H
[100%] About to build the REFPROP.h header file w/ /usr/bin/python;-u;/REFPROP-cmake/externals/REFPROP-headers/generate_header.py;--FORTRAN-path;/shared/RP10src/DLLFILES;--python-exe;/usr/bin/python
Writing the .pyf file with numpy.f2py, please be patient...
About to run: /usr/bin/python -m numpy.f2py --quiet --no-lower -h REFPROP.pyf /shared/RP10src/DLLFILES/PASS_FTN.FOR
numpy version: 1.19.5
Deleting REFPROP.pyf
[100%] Built target REFPROP_H
root@9345bffc20f1:/#

Answer 6 · 2022-06-16T14:22:16.000Z

Fixed README. You should be using 20.04, or 22.04

Answer 7 · 2022-06-16T14:22:39.000Z

Yes, seems so

Answer 8 · 2022-06-16T14:24:36.000Z

@ianhbell when you say I should using 20.04, or 22.04
were you referring to you example Dockerfile https://github.com/usnistgov/REFPROP-cmake/blob/master/docker/ubuntu-18.04/Dockerfile#L1 ?

Or the host os running docker system?

Answer 9 · 2022-06-16T14:25:37.000Z

I mean the base image, 18.04 is quite old now, and better to stay up to date since that gives you more modern python versions, etc.

Answer 10 · 2022-06-16T14:25:53.000Z

cool I'll try that now.

Answer 11 · 2022-06-16T14:38:01.000Z

so far one snag I hit w/20.04 as the base image was the build asks for tzdata region selection and prompts for input.
Still trying to figure out how to avoid that prompt... also making a selection upon prompt seems to freeze the build process.

Answer 12 · 2022-06-16T14:39:26.000Z

you can set the DEBIAN_NONINTERACTIVE environment variable to avoid that problem

Answer 13 · 2022-06-16T14:40:03.000Z

e.g.: https://github.com/usnistgov/REFPROP-tests/blob/master/docker/test/Dockerfile

Answer 14 · 2022-06-16T14:56:00.000Z

That was helpful, thanks. Can you confirm a few things for me...

my Dockerfile

FROM ubuntu:20.04

RUN apt-get -y -m update && \
    DEBIAN_FRONTEND=noninteractive apt-get install -y git cmake g++ gfortran python3 python3-pip python3-six

# This ADD block forces a build (invalidates the cache) if the git repo contents have changed, otherwise leaves it untouched.
ADD https://api.github.com/repos/usnistgov/REFPROP-cmake/git/refs/heads/master RPcmake-version.json
RUN git clone --recursive https://github.com/usnistgov/REFPROP-cmake && \
    cd REFPROP-cmake/ && \
    mkdir build && \
    cd build/

# Soft-link pip3->pip and same for python
RUN  ln -s /usr/bin/python3 /usr/bin/python


# Install numpy from pip
RUN pip install numpy && python -c "import numpy; print(numpy.__version__)"

COPY ./run-me-inside-container.sh ./build.sh

and my build output (since i'm not familiar with FORTRAN or refprop) I see some Warning's

root@95d6d241db0f:/# ./build.sh 
-- The C compiler identification is GNU 9.4.0
-- The CXX compiler identification is GNU 9.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- The Fortran compiler identification is GNU 9.4.0
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Found PythonInterp: /usr/bin/python (found version "3.8.10") 
-- DEFSYM_FLAG: --using-defsym
-- linux
Missing from PASS_CMN_tokens:  ['ABFLASHdll', 'VIRBCD12dll', 'VIRTAUdll']
Missing from REFPROP_lib.h: []

-- Configuring done
-- Generating done
-- Build files have been written to: /REFPROP-cmake/build
Scanning dependencies of target REFPROP_H
[  6%] About to build the REFPROP.h header file w/ /usr/bin/python;-u;/REFPROP-cmake/externals/REFPROP-headers/generate_header.py;--FORTRAN-path;/shared/RP10src/DLLFILES;--python-exe;/usr/bin/python
Writing the .pyf file with numpy.f2py, please be patient...
About to run: /usr/bin/python -m numpy.f2py --quiet --no-lower -h REFPROP.pyf /shared/RP10src/DLLFILES/PASS_FTN.FOR
numpy version: 1.22.4
Deleting REFPROP.pyf
[  6%] Built target REFPROP_H
Scanning dependencies of target refprop
[ 12%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/CORE_ANC.FOR.o
[ 18%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/CORE_FEQ.FOR.o
[ 25%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/CORE_PR.FOR.o
[ 31%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/FLSH_SUB.FOR.o
[ 37%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/MIX_HMX.FOR.o
[ 43%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/PROP_SUB.FOR.o
[ 50%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/REFPROP.FOR.o
/shared/RP10src/REFPROP.FOR:5589:72:

 5589 |         if (ABS(iErrPrnt).eq.3) pause           !If your compiler complains about this line, just delete it.
      |                                                                       1

Warning: Deleted feature: PAUSE statement at (1)
/shared/RP10src/REFPROP.FOR:3108:0:

 3108 |       if (iUCode.eq.1000) hun=hUnt(4)(2:ispc(4)-1)         !Remove parenthesis if output units is only J/mol or kJ/kg.
      | 
Warning: '__builtin_memcpy' reading 255 bytes from a region of size 39 [-Wstringop-overflow=]
/shared/RP10src/REFPROP.FOR:3109:0:

 3109 |       if (iUCode.eq.0100) hun=hUnt(3)(2:ispc(3)-1)         !Same for density (mol/dm^3 or kg/m^3).
      | 
Warning: '__builtin_memcpy' reading 255 bytes from a region of size 59 [-Wstringop-overflow=]
/shared/RP10src/REFPROP.FOR:3110:0:

 3110 |       if (iUCode.eq.0900) hun=hUnt(0)(2:ispc(0)-1)         !Same for volume.
      | 
Warning: '__builtin_memcpy' reading 255 bytes from a region of size 119 [-Wstringop-overflow=]
[ 56%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/SAT_SUB.FOR.o
[ 62%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/SETUP.FOR.o
[ 68%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/TRNSP.FOR.o
[ 75%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/TRNS_TCX.FOR.o
[ 81%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/TRNS_VIS.FOR.o
[ 87%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/UTILITY.FOR.o
[ 93%] Building Fortran object CMakeFiles/refprop.dir/shared/RP10src/DLLFILES/PASS_FTN.FOR.o
[100%] Linking Fortran shared library librefprop.so
[100%] Built target refprop

Answer 15 · 2022-06-16T14:57:26.000Z

That all seems ok with me

Answer 16 · 2022-06-16T14:58:26.000Z

Cool, thanks. I'll close the issue.